[gmx-users] Bug in free energy calculations in, heme-containing systems

Chris Oostenbrink c.oostenbrink at few.vu.nl
Wed Oct 26 08:35:08 CEST 2005

> The reason for all this probably lies in grompp, where the standard 
> force-field parameters are incorporated into the system topology, 
> resulting in a faulty tpr-file. In the case where the Heme group is not 
> coordinated to a His, commenting out the default force-field parameters 
> in file ffG43a1bon.itp seems to help. Otherwise, explicitly stating all 
> Heme parameters in state B as well may also prevent the error from 
> happening.

Since you reported this previously it has been discussed on one of the
mailing lists. Berk Hess has implemented a fix for this behavior in
grompp which will be in 3.3.1. Check the discussion on the gmx-revision


Dear David,

No, this is not the same bug as the one I reported a couple of weeks 
ago. This is a new one. I hope that the fix Berk implemented was in 
runmd, more specifically in gmxlib/bondsfree.c
What I am reporting now is a hidden mix-up of parameters in the tpr-file 
due to grompp. It affects any free energy calculation in systems that 
contain a heme group. I did not dig into the code myself this time, but 
suggested two work-arounds in my previous mail. Please read it carefully.


Chris Oostenbrink

Computational Medicinal Chemistry and Toxicology
Department of Pharmacochemistry
Vrije Universiteit                                  Tel: + 31 20 5987606
De Boelelaan 1083 P 262                             Fax: + 31 20 5987610
NL-1081 HV Amsterdam
The Netherlands                          e-mail: c.oostenbrink at few.vu.nl

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